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Yorodumi- PDB-7wj7: Crystal Structure of the Kinase Domain with Adenosine of a Class ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wj7 | |||||||||
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Title | Crystal Structure of the Kinase Domain with Adenosine of a Class III Lanthipeptide Synthetase CurKC | |||||||||
Components | Serine/threonine protein kinase | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / Lanthipeptide Synthetase / Class III / CurKC / curvopeptin | |||||||||
Function / homology | Function and homology information carbohydrate metabolic process / protein phosphorylation / protein serine/threonine kinase activity / ATP binding Similarity search - Function | |||||||||
Biological species | Thermomonospora curvata (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | |||||||||
Authors | Huang, S. / Wang, H. | |||||||||
Funding support | China, 2items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022 Title: Discovery of a Unique Structural Motif in Lanthipeptide Synthetases for Substrate Binding and Interdomain Interactions. Authors: Huang, S. / Wang, Y. / Cai, C. / Xiao, X. / Liu, S. / Ma, Y. / Xie, X. / Liang, Y. / Chen, H. / Zhu, J. / Hegemann, J.D. / Yao, H. / Wei, W. / Wang, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wj7.cif.gz | 110.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wj7.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 7wj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wj7_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7wj7_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7wj7_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 7wj7_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/7wj7 ftp://data.pdbj.org/pub/pdb/validation_reports/wj/7wj7 | HTTPS FTP |
-Related structure data
Related structure data | 7wj6C 1mruS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30178.303 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Adenosine Source: (gene. exp.) Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / KCTC 9072 / NBRC 15933 / NCIMB 10081 / Henssen B9) (bacteria) Strain: ATCC 19995 / DSM 43183 / JCM 3096 / KCTC 9072 / NBRC 15933 / NCIMB 10081 / Henssen B9 Gene: Tcur_3610 / Production host: Escherichia coli (E. coli) / References: UniProt: D1ABX1 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.9 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M Bis-Tris, pH 6.0, 3.0 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→19.82 Å / Num. obs: 20611 / % possible obs: 99.98 % / Redundancy: 19.8 % / CC1/2: 0.999 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.55→2.66 Å / Mean I/σ(I) obs: 5 / Num. unique obs: 2487 / CC1/2: 0.947 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MRU Resolution: 2.55→19.82 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.68 Å2 / Biso mean: 57.2492 Å2 / Biso min: 25.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→19.82 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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